I have read your question a couple of times and it looks like you have checked or replaced the master cylinder and wheel cylinders. One of the areas of concern to me is that when you try to source a master cylinder for a '69 with power front disc brakes, no one lists one. My '69 has power front disc brakes with a 4 speed manual. It is currently apart to be restored but the guy I bought it from encountered the same problem that you have described. He rebuilt his using a kit from someone and it basically did just as you have described. I have not attempted to rebuild mine yet - I have planned on sending it to one of the professional brake booster and master cylinder restorers because of access to the correct seals, springs, etc.
Have you noticed whether or not the front brakes stay "engaged" after you have pushed the pedal to the floor or do they release immediately and the pedal comes back up immediately? If they do not release immediately, take a look at the front flexible brake hoses. I don't really think thats what it is, but it doesn't hurt to double check.
I think that you probably have a master cylinder problem but have you checked the booster? I am very suspicous of the guy telling you he replaced both. What happened to the originals? Like I said earlier - I tend to think that parts are not readily available for a '69 with this brake/trans set up.
I plan to go up to the attic and measure the brake rod for you, but I need to move some stuff. Maybe later tonight or tomorrow.
